I have EXTRA_ECONF="--disable-dependency-tracking" since 5-6 years and no package complained.
* During Perl build, EXTRA_ECONF= --disable-dependency-tracking
Configure: unknown option --disable-dependency-tracking
Usage: Configure [-dehrsEKOSV] [-f config.sh] [-D symbol] [-D symbol=value]
[-U symbol] [-U symbol=] [-A command:symbol...]
If you think there is something that can be done, like unset EXTRA_ECONF, otherwise feel free to close.
Perl's Configure is not autoconf-based, but a separate development and incompatible (and likely much older). So I fear there's not much we can do.
Actually we disabled EXTRA_ECONF because of that (I think), but people complained then, so I re-enabled it recently...